PyPI - biotite - Versions diffs - 0.39.0__cp312-cp312-win_amd64.whl → 0.40.0__cp312-cp312-win_amd64.whl - Mend

biotite 0.39.0__cp312-cp312-win_amd64.whl → 0.40.0__cp312-cp312-win_amd64.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.

This version of biotite might be problematic. Click here for more details.

Files changed (104) hide show

biotite/__init__.py +3 -3
biotite/application/dssp/app.py +18 -18
biotite/database/rcsb/download.py +19 -14
biotite/sequence/align/banded.c +256 -235
biotite/sequence/align/banded.cp312-win_amd64.pyd +0 -0
biotite/sequence/align/kmeralphabet.c +241 -220
biotite/sequence/align/kmeralphabet.cp312-win_amd64.pyd +0 -0
biotite/sequence/align/kmersimilarity.c +213 -194
biotite/sequence/align/kmersimilarity.cp312-win_amd64.pyd +0 -0
biotite/sequence/align/kmertable.cp312-win_amd64.pyd +0 -0
biotite/sequence/align/kmertable.cpp +231 -203
biotite/sequence/align/localgapped.c +256 -235
biotite/sequence/align/localgapped.cp312-win_amd64.pyd +0 -0
biotite/sequence/align/localungapped.c +233 -212
biotite/sequence/align/localungapped.cp312-win_amd64.pyd +0 -0
biotite/sequence/align/multiple.c +253 -232
biotite/sequence/align/multiple.cp312-win_amd64.pyd +0 -0
biotite/sequence/align/pairwise.c +272 -251
biotite/sequence/align/pairwise.cp312-win_amd64.pyd +0 -0
biotite/sequence/align/permutation.c +213 -194
biotite/sequence/align/permutation.cp312-win_amd64.pyd +0 -0
biotite/sequence/align/selector.c +215 -195
biotite/sequence/align/selector.cp312-win_amd64.pyd +0 -0
biotite/sequence/align/tracetable.c +213 -193
biotite/sequence/align/tracetable.cp312-win_amd64.pyd +0 -0
biotite/sequence/codec.c +233 -212
biotite/sequence/codec.cp312-win_amd64.pyd +0 -0
biotite/sequence/phylo/nj.c +213 -194
biotite/sequence/phylo/nj.cp312-win_amd64.pyd +0 -0
biotite/sequence/phylo/tree.c +225 -200
biotite/sequence/phylo/tree.cp312-win_amd64.pyd +0 -0
biotite/sequence/phylo/upgma.c +213 -194
biotite/sequence/phylo/upgma.cp312-win_amd64.pyd +0 -0
biotite/structure/basepairs.py +7 -12
biotite/structure/bonds.c +1173 -1224
biotite/structure/bonds.cp312-win_amd64.pyd +0 -0
biotite/structure/celllist.c +215 -195
biotite/structure/celllist.cp312-win_amd64.pyd +0 -0
biotite/structure/charges.c +1050 -1099
biotite/structure/charges.cp312-win_amd64.pyd +0 -0
biotite/structure/filter.py +30 -37
biotite/structure/info/__init__.py +5 -8
biotite/structure/info/atoms.py +25 -67
biotite/structure/info/bonds.py +46 -100
biotite/structure/info/ccd/README.rst +8 -0
biotite/structure/info/ccd/amino_acids.txt +1646 -0
biotite/structure/info/ccd/carbohydrates.txt +1133 -0
biotite/structure/info/ccd/components.bcif +0 -0
biotite/structure/info/ccd/nucleotides.txt +797 -0
biotite/structure/info/ccd.py +95 -0
biotite/structure/info/groups.py +90 -0
biotite/structure/info/masses.py +21 -20
biotite/structure/info/misc.py +11 -22
biotite/structure/info/standardize.py +17 -12
biotite/structure/io/__init__.py +2 -4
biotite/structure/io/ctab.py +1 -1
biotite/structure/io/general.py +37 -43
biotite/structure/io/mmtf/__init__.py +3 -0
biotite/structure/io/mmtf/convertarray.c +217 -196
biotite/structure/io/mmtf/convertarray.cp312-win_amd64.pyd +0 -0
biotite/structure/io/mmtf/convertfile.c +215 -195
biotite/structure/io/mmtf/convertfile.cp312-win_amd64.pyd +0 -0
biotite/structure/io/mmtf/decode.c +223 -202
biotite/structure/io/mmtf/decode.cp312-win_amd64.pyd +0 -0
biotite/structure/io/mmtf/encode.c +213 -194
biotite/structure/io/mmtf/encode.cp312-win_amd64.pyd +0 -0
biotite/structure/io/mmtf/file.py +34 -26
biotite/structure/io/npz/__init__.py +3 -0
biotite/structure/io/npz/file.py +21 -18
biotite/structure/io/pdb/__init__.py +3 -3
biotite/structure/io/pdb/file.py +5 -3
biotite/structure/io/pdb/hybrid36.c +63 -43
biotite/structure/io/pdb/hybrid36.cp312-win_amd64.pyd +0 -0
biotite/structure/io/pdbqt/file.py +32 -32
biotite/structure/io/pdbx/__init__.py +13 -6
biotite/structure/io/pdbx/bcif.py +649 -0
biotite/structure/io/pdbx/cif.py +1028 -0
biotite/structure/io/pdbx/component.py +243 -0
biotite/structure/io/pdbx/convert.py +707 -359
biotite/structure/io/pdbx/encoding.c +112803 -0
biotite/structure/io/pdbx/encoding.cp312-win_amd64.pyd +0 -0
biotite/structure/io/pdbx/error.py +14 -0
biotite/structure/io/pdbx/legacy.py +267 -0
biotite/structure/molecules.py +151 -151
biotite/structure/sasa.c +213 -194
biotite/structure/sasa.cp312-win_amd64.pyd +0 -0
biotite/structure/superimpose.py +158 -115
{biotite-0.39.0.dist-info → biotite-0.40.0.dist-info}/METADATA +2 -2
{biotite-0.39.0.dist-info → biotite-0.40.0.dist-info}/RECORD +92 -90
{biotite-0.39.0.dist-info → biotite-0.40.0.dist-info}/WHEEL +1 -1
biotite/structure/info/amino_acids.json +0 -1556
biotite/structure/info/amino_acids.py +0 -42
biotite/structure/info/carbohydrates.json +0 -1122
biotite/structure/info/carbohydrates.py +0 -39
biotite/structure/info/intra_bonds.msgpack +0 -0
biotite/structure/info/link_types.msgpack +0 -1
biotite/structure/info/nucleotides.json +0 -772
biotite/structure/info/nucleotides.py +0 -39
biotite/structure/info/residue_masses.msgpack +0 -0
biotite/structure/info/residue_names.msgpack +0 -3
biotite/structure/info/residues.msgpack +0 -0
biotite/structure/io/pdbx/file.py +0 -652
{biotite-0.39.0.dist-info → biotite-0.40.0.dist-info}/LICENSE.rst +0 -0
{biotite-0.39.0.dist-info → biotite-0.40.0.dist-info}/top_level.txt +0 -0

biotite/structure/info/ccd/carbohydrates.txt ADDED Viewed

@@ -0,0 +1,1133 @@
+045
+05L
+07E
+07Y
+08U
+09X
+0AT
+0BD
+0H0
+0HX
+0LP
+0MK
+0NZ
+0TS
+0UB
+0V4
+0WK
+0XY
+0YT
+10M
+12E
+145
+147
+149
+14T
+15L
+16F
+16G
+16O
+17T
+18D
+18O
+18T
+1AR
+1BW
+1CF
+1FT
+1GL
+1GN
+1JB
+1LL
+1NA
+1S3
+1S4
+1SD
+1X4
+20S
+20X
+22O
+22S
+23V
+24S
+25E
+26M
+26O
+26Q
+26R
+26V
+26W
+26Y
+27C
+289
+291
+293
+2DG
+2DR
+2F8
+2FG
+2FL
+2FP
+2GL
+2GS
+2H5
+2HA
+2M4
+2M5
+2M8
+2OS
+2SI
+2WP
+2WS
+32O
+34V
+38J
+3BU
+3CM
+3DO
+3DY
+3FM
+3GR
+3HD
+3J3
+3J4
+3LJ
+3LR
+3MF
+3MG
+3MK
+3R3
+3S6
+3SA
+3YW
+40J
+42D
+445
+44S
+46D
+46M
+46Z
+475
+48Z
+491
+49A
+49S
+49T
+49V
+4AM
+4CQ
+4GC
+4GL
+4GP
+4JA
+4N2
+4NN
+4QY
+4R1
+4RS
+4SG
+4U0
+4U1
+4U2
+4UZ
+4V5
+50A
+510
+51N
+56N
+57S
+5DI
+5GF
+5GO
+5II
+5KQ
+5KS
+5KT
+5KV
+5L2
+5L3
+5LS
+5LT
+5MM
+5N6
+5QP
+5RP
+5SA
+5SP
+5TH
+5TJ
+5TK
+5TM
+604
+61J
+62I
+64K
+66O
+6BG
+6C2
+6DM
+6GB
+6GP
+6GR
+6K3
+6KH
+6KL
+6KS
+6KU
+6KW
+6LA
+6LS
+6LW
+6MJ
+6MN
+6PG
+6PY
+6PZ
+6S2
+6SA
+6UD
+6Y6
+6YR
+6ZC
+73E
+79J
+7CV
+7D1
+7GP
+7JZ
+7K2
+7K3
+7NU
+7SA
+83Y
+89Y
+8B7
+8B9
+8EX
+8GA
+8GG
+8GP
+8I4
+8LM
+8LR
+8OQ
+8PK
+8S0
+8YV
+95Z
+96O
+98U
+9AM
+9C1
+9CD
+9GP
+9KJ
+9MR
+9OK
+9PG
+9QG
+9QZ
+9RN
+9S7
+9SG
+9SJ
+9SM
+9SP
+9T1
+9T7
+9VP
+9WJ
+9WN
+9WZ
+9YW
+A0K
+A1Q
+A2G
+A5C
+A6P
+AAL
+AAO
+ABC
+ABD
+ABE
+ABF
+ABL
+AC1
+ACG
+ACR
+ACX
+ADA
+ADG
+ADR
+AF1
+AFD
+AFL
+AFO
+AFP
+AFR
+AGC
+AGH
+AGL
+AGR
+AH2
+AH8
+AHG
+AHM
+AHR
+AIG
+ALL
+ALX
+AMG
+AMN
+AMU
+AMV
+ANA
+AOG
+AOS
+AQA
+ARA
+ARB
+ARE
+ARI
+ARW
+ASC
+ASG
+ASO
+AXP
+AXR
+AY9
+AZC
+B0D
+B16
+B1H
+B1N
+B2G
+B4G
+B6D
+B7G
+B8D
+B9D
+BBK
+BBV
+BCD
+BCW
+BDF
+BDG
+BDP
+BDR
+BDZ
+BEM
+BFN
+BFP
+BG6
+BG8
+BGC
+BGL
+BGN
+BGP
+BGS
+BHG
+BM3
+BM7
+BMA
+BMX
+BND
+BNG
+BNX
+BO1
+BOG
+BQY
+BRI
+BS7
+BTG
+BTU
+BW3
+BWG
+BXF
+BXP
+BXX
+BXY
+BZD
+C3B
+C3G
+C3X
+C4B
+C4W
+C4X
+C5X
+CAP
+CBF
+CBI
+CBK
+CDR
+CE5
+CE6
+CE8
+CEG
+CEX
+CEY
+CEZ
+CGF
+CJB
+CKB
+CKP
+CNP
+CR1
+CR6
+CRA
+CT3
+CTO
+CTR
+CTT
+D0N
+D1M
+D5E
+D6G
+DAF
+DAG
+DAN
+DDA
+DDB
+DDL
+DEG
+DEL
+DFR
+DFX
+DG0
+DGC
+DGD
+DGM
+DGO
+DGS
+DGU
+DIG
+DJB
+DJE
+DK4
+DKX
+DKZ
+DL6
+DLD
+DLF
+DLG
+DMU
+DNO
+DO8
+DOM
+DP5
+DPC
+DQQ
+DQR
+DR2
+DR3
+DR4
+DR5
+DRI
+DSR
+DT6
+DVC
+DYM
+E3M
+E4P
+E5G
+EAG
+EBG
+EBQ
+EEN
+EEQ
+EGA
+EJT
+EMP
+EMZ
+EPG
+EQP
+EQV
+ERE
+ERI
+ETT
+EUS
+F1P
+F1X
+F55
+F58
+F6P
+F8X
+FBP
+FCA
+FCB
+FCT
+FDP
+FDQ
+FFC
+FFX
+FIF
+FIX
+FK9
+FKD
+FMF
+FMO
+FNG
+FNY
+FRU
+FSA
+FSI
+FSM
+FSR
+FSW
+FU4
+FUB
+FUC
+FUD
+FUF
+FUL
+FUY
+FVQ
+FX1
+FYJ
+G0S
+G16
+G1P
+G20
+G28
+G2F
+G3F
+G3I
+G4D
+G4S
+G6D
+G6P
+G6S
+G7P
+G8Z
+GAA
+GAC
+GAD
+GAF
+GAL
+GAT
+GBH
+GC1
+GC4
+GC9
+GCB
+GCD
+GCN
+GCO
+GCS
+GCT
+GCU
+GCV
+GCW
+GDA
+GDL
+GE1
+GE3
+GFP
+GIV
+GL0
+GL1
+GL2
+GL4
+GL5
+GL6
+GL7
+GL9
+GLA
+GLB
+GLC
+GLD
+GLF
+GLG
+GLO
+GLP
+GLS
+GLT
+GLW
+GM0
+GMB
+GMH
+GMT
+GMZ
+GN1
+GN4
+GNS
+GNX
+GP0
+GP1
+GP4
+GPH
+GPK
+GPM
+GPO
+GPQ
+GPU
+GPV
+GPW
+GQ1
+GRF
+GRX
+GS1
+GS4
+GS9
+GSA
+GSD
+GTE
+GTH
+GTK
+GTM
+GTR
+GU0
+GU1
+GU2
+GU3
+GU4
+GU5
+GU6
+GU8
+GU9
+GUF
+GUL
+GUP
+GUZ
+GXL
+GXV
+GYE
+GYG
+GYP
+GYU
+GYV
+GZL
+H1M
+H1S
+H2P
+H3S
+H53
+H6Q
+H6Z
+HBZ
+HD4
+HDL
+HMS
+HNV
+HNW
+HSG
+HSH
+HSJ
+HSQ
+HSR
+HSU
+HSX
+HSY
+HSZ
+HTG
+HTM
+HVC
+I57
+IAB
+IDC
+IDF
+IDG
+IDR
+IDS
+IDT
+IDU
+IDX
+IDY
+IEM
+IN1
+IPT
+ISD
+ISL
+ISX
+IVG
+IXD
+J5B
+JFZ
+JHM
+JLT
+JRV
+JS2
+JSV
+JV4
+JVA
+JVS
+JZR
+K5B
+K99
+KBA
+KBG
+KD5
+KDA
+KDB
+KDD
+KDE
+KDF
+KDM
+KDN
+KDO
+KDR
+KFN
+KG1
+KGM
+KHP
+KME
+KO1
+KO2
+KOT
+KQC
+KTU
+L1L
+L6N
+L6S
+L6T
+LAG
+LAH
+LAI
+LAK
+LAO
+LAT
+LB2
+LBS
+LBT
+LCN
+LDY
+LEC
+LER
+LFC
+LFR
+LGC
+LGU
+LKA
+LKS
+LM2
+LMO
+LMT
+LMU
+LNV
+LOG
+LOX
+LPK
+LRH
+LSM
+LTG
+LTM
+LVO
+LVZ
+LXB
+LXC
+LXZ
+LZ0
+M1F
+M1P
+M2F
+M3M
+M3N
+M55
+M6D
+M6P
+M7B
+M7P
+M8C
+MA1
+MA2
+MA3
+MA8
+MAB
+MAF
+MAG
+MAL
+MAN
+MAT
+MAV
+MAW
+MBE
+MBF
+MBG
+MCU
+MDA
+MDP
+MFA
+MFB
+MFU
+MG5
+MGA
+MGC
+MGL
+MGS
+MJJ
+MLB
+MLR
+MMA
+MMN
+MN0
+MNA
+MQG
+MQT
+MRH
+MRP
+MSX
+MTT
+MUB
+MUG
+MUR
+MVP
+MXY
+MXZ
+MYG
+N1L
+N3U
+N9S
+NA1
+NAA
+NAG
+NBG
+NBX
+NBY
+NDG
+NED
+NFG
+NG1
+NG6
+NGA
+NGB
+NGC
+NGE
+NGF
+NGK
+NGL
+NGR
+NGS
+NGY
+NGZ
+NHF
+NLC
+NM6
+NM9
+NNG
+NPF
+NSQ
+NT1
+NTF
+NTO
+NTP
+NXD
+NYT
+O1G
+OAK
+OEL
+OI7
+OPM
+ORP
+OSU
+OTG
+OTN
+OTU
+OX2
+P53
+P6P
+P8E
+PA1
+PA5
+PAV
+PDX
+PH5
+PKM
+PNA
+PNG
+PNJ
+PNW
+PPC
+PRP
+PSG
+PSJ
+PSV
+PTQ
+PUF
+PZU
+QDK
+QIF
+QKH
+QPS
+QV4
+R1P
+R1X
+R2B
+R2G
+R5P
+RAA
+RAE
+RAF
+RAM
+RAO
+RAT
+RB5
+RBL
+RCD
+RDP
+REL
+RER
+RF5
+RG1
+RGG
+RHA
+RHC
+RI2
+RIB
+RIP
+RM4
+RNS
+RNT
+ROB
+ROR
+RP3
+RP5
+RP6
+RPA
+RR7
+RRJ
+RRY
+RST
+RTG
+RTV
+RUB
+RUG
+RUU
+RV7
+RVG
+RVM
+RWI
+RY7
+RZM
+S6P
+S7P
+S81
+SA0
+SCG
+SCR
+SDD
+SDY
+SEJ
+SF6
+SF9
+SFJ
+SFU
+SG4
+SG5
+SG6
+SG7
+SGA
+SGC
+SGD
+SGN
+SGS
+SHB
+SHD
+SHG
+SI3
+SIA
+SID
+SIO
+SIZ
+SLB
+SLM
+SLT
+SMD
+SN5
+SNG
+SOE
+SOG
+SOL
+SOR
+SR1
+SSG
+SSH
+STW
+STZ
+SUC
+SUP
+SUS
+SWE
+SZZ
+T68
+T6D
+T6P
+T6T
+TA6
+TAG
+TCB
+TCG
+TDG
+TEU
+TF0
+TFU
+TGA
+TGK
+TGR
+TGY
+TH1
+TM5
+TM6
+TM9
+TMR
+TMX
+TNX
+TOA
+TOC
+TQY
+TRE
+TRV
+TS8
+TT7
+TTV
+TTZ
+TU4
+TUG
+TUJ
+TUP
+TUR
+TVD
+TVG
+TVM
+TVS
+TVV
+TVY
+TW7
+TWA
+TWD
+TWG
+TWJ
+TWY
+TXB
+TY6
+TYV
+U1Y
+U2A
+U2D
+U63
+U8V
+U97
+U9A
+U9D
+U9G
+U9J
+U9M
+UAP
+UBH
+UBO
+UCD
+UDC
+UEA
+V3M
+V3P
+V71
+VDF
+VG1
+VJ1
+VJ4
+VKN
+VTB
+W9T
+WIA
+WOO
+WUN
+WZ1
+WZ2
+WZ4
+X0X
+X1P
+X1X
+X2F
+X2Y
+X34
+X4S
+X5S
+X6X
+X6Y
+XBP
+XDP
+XDX
+XGP
+XIL
+XKJ
+XLF
+XLS
+XMM
+XS2
+XUL
+XXM
+XXR
+XXX
+XY6
+XY9
+XYB
+XYF
+XYL
+XYP
+XYS
+XYT
+XYZ
+YDR
+YIO
+YJM
+YKR
+YO5
+YX0
+YX1
+YYB
+YYD
+YYH
+YYJ
+YYK
+YYM
+YYQ
+YYR
+YZ0
+YZT
+Z0F
+Z15
+Z16
+Z2D
+Z2T
+Z3K
+Z3L
+Z3Q
+Z3U
+Z4K
+Z4R
+Z4S
+Z4U
+Z4V
+Z4W
+Z4Y
+Z57
+Z5J
+Z5L
+Z61
+Z6G
+Z6H
+Z6J
+Z6W
+Z8H
+Z8T
+Z9D
+Z9E
+Z9H
+Z9K
+Z9L
+Z9M
+Z9N
+Z9W
+ZB0
+ZB1
+ZB2
+ZB3
+ZCD
+ZCZ
+ZD0
+ZDC
+ZDM
+ZDO
+ZEE
+ZEL
+ZGE
+ZMR